Dear Gordon, i performed 8 technical replicates with two color oligo array. Particularly i have 3 samples: MUT1, MUT2 and Reference (pool of wild type mice), then my experiments were MUT1 vs REFERENCE (4replicates with 2 dye swap) and the same for MUT2 (MUT2 vs REFERENCE). Then i analyzed with genepix and with limma or limmaGUI. My question is: can i perform a comparison etween MUT1 vs MUT2 using a parameterization MUT1 minus MUT2? If i do this, how thw M values are computed? or is it better compute a contrast matrix?? thanks a lot, andrea Andrea Bozzato, PhD Student Dip. Scienze Biomediche e Biotecnologie Sez. Biologia e genetica V.le Europa, 11 25123 Brescia ITALY ------------------------------------------------------------ Sei stanco di girare a vuoto? Con il nuovo motore di ricerca Interfree trovi di tutto. Vieni a trovarci: http://search.interfree.it/